Contacts of the helix formed by residues 310 - 331 (chain D) in PDB entry 1FM6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309D LEU* 1.3 73.5 - - - +
311D LEU* 1.3 63.3 + - - +
312D ASN* 3.0 37.0 + - - +
313D ASP* 2.8 39.6 + - - +
314D GLN* 2.9 10.6 + - - +
401D LEU* 4.0 21.0 - - - +
402D ASN* 4.1 17.9 + - - +
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU 3.2 3.6 + - - -
310D ASP* 1.3 74.7 + - - +
312D ASN* 1.3 63.2 + - - +
314D GLN* 3.3 28.7 + - - +
315D VAL* 3.3 21.5 + - - +
691E HIS* 3.6 31.6 - - + +
694E LEU* 4.2 20.2 - - + -
695E GLN* 4.6 22.2 - - + +
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Residues in contact with ASN 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ASP* 3.0 20.1 + - - +
311D LEU* 1.3 80.4 - - - +
313D ASP* 1.3 63.8 + - - +
315D VAL* 3.6 6.9 + - - +
316D THR* 3.1 27.5 + - - -
401D LEU* 4.2 19.0 - - + +
686E ARG* 4.0 19.8 + - - -
691E HIS* 4.5 5.1 + - - -
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Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 4.9 7.7 - - + +
310D ASP* 2.8 26.3 + - + +
312D ASN* 1.3 77.7 - - - +
314D GLN* 1.3 65.4 + - - +
316D THR* 3.2 2.1 + - - -
317D LEU* 3.0 30.4 + - - +
399D GLY 4.6 0.7 - - - +
400D LEU* 3.6 19.8 - - + -
401D LEU* 2.7 33.2 + - - +
402D ASN* 3.0 36.7 + - - +
406D ILE* 4.4 8.2 - - + +
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Residues in contact with GLN 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D PHE* 3.4 55.2 + - + +
307D VAL* 3.4 26.1 + - - +
309D LEU* 3.2 25.9 + - + +
310D ASP 2.9 11.2 + - - +
311D LEU* 3.5 27.7 - - - +
312D ASN 3.3 0.2 - - - -
313D ASP* 1.3 78.6 - - - +
315D VAL* 1.3 61.4 + - - +
317D LEU* 3.4 0.9 + - - +
318D LEU* 3.2 19.9 + - - +
694E LEU* 3.4 28.7 - - + +
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU 3.3 13.8 + - - +
312D ASN* 3.9 6.1 - - - +
313D ASP 3.2 0.4 - - - -
314D GLN* 1.3 75.1 - - - +
316D THR* 1.3 55.1 + - - +
318D LEU* 3.2 5.2 + - - +
319D LYS* 2.7 33.1 + - + +
686E ARG 5.3 0.2 - - - +
687E HIS* 3.6 39.7 - - + +
690E LEU* 3.7 14.8 - - + -
691E HIS* 3.9 28.0 - - + +
694E LEU* 3.4 24.5 - - + -
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Residues in contact with THR 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ASN 3.1 18.9 + - - -
313D ASP* 3.6 5.2 + - - -
315D VAL* 1.3 76.2 - - - +
317D LEU* 1.3 63.4 + - - +
319D LYS* 4.0 8.9 - - - +
320D TYR* 3.1 32.0 + - + +
397D ARG* 3.7 12.9 - - + +
398D PRO 3.7 23.2 + - - +
399D GLY 4.5 8.7 + - - -
400D LEU* 3.7 24.9 - - + +
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Residues in contact with LEU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D PHE* 3.7 30.1 - - + -
309D LEU* 4.3 9.2 - - + -
313D ASP 3.0 19.0 + - - +
314D GLN 3.6 5.4 - - - +
316D THR* 1.3 77.5 - - - +
318D LEU* 1.3 59.2 + - - +
321D GLY* 2.9 28.8 + - - -
392D ILE* 3.5 32.6 - - + +
393D LEU* 4.4 8.5 - - + -
394D SER 3.6 22.4 - - - +
397D ARG* 3.9 9.5 + - + -
400D LEU* 3.7 20.2 - - + -
406D ILE* 4.0 18.4 - - + -
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D ILE* 5.1 5.8 - - + -
297D THR* 4.1 24.9 - - + +
300D ALA* 3.8 27.1 - - + -
306D PHE* 4.2 4.9 - - + -
314D GLN 3.2 18.5 + - - +
315D VAL* 3.6 5.8 - - - +
317D LEU* 1.3 76.0 - - - +
319D LYS* 1.3 61.6 + - - +
322D VAL* 2.8 44.2 + - + +
392D ILE* 4.5 10.8 - - + -
472D ILE* 6.0 0.2 - - - -
690E LEU* 4.3 18.2 - - + -
694E LEU* 3.5 41.7 - - + -
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Residues in contact with LYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D VAL 2.7 21.4 + - - +
316D THR* 3.5 10.5 - - - +
318D LEU* 1.3 75.2 - - - +
320D TYR* 1.3 78.1 + - + +
322D VAL* 4.5 2.6 + - - +
323D HIS* 4.8 2.6 + - - +
471D GLU 3.2 5.1 + - - -
472D ILE* 2.9 53.7 + - - +
474D LYS 3.0 23.5 + - - -
475D ASP* 4.7 2.7 - - - -
476D LEU* 3.7 22.6 - - + +
687E HIS* 2.5 45.7 + - + +
690E LEU* 4.2 11.8 - - + +
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Residues in contact with TYR 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D THR* 3.1 33.3 + - + +
319D LYS* 1.3 95.6 - - + +
321D GLY* 1.3 63.2 + - - +
323D HIS* 4.5 3.1 + - - +
324D GLU* 3.8 7.8 + - - +
397D ARG* 3.3 36.5 + - + +
398D PRO* 3.6 45.1 + - + +
446D VAL* 5.7 0.3 - - - +
475D ASP 3.7 17.8 + - - -
476D LEU* 3.4 27.2 - - + -
477D TYR* 3.7 53.6 + + + +
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Residues in contact with GLY 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D LEU 2.9 19.1 + - - -
318D LEU* 5.3 0.2 - - - -
320D TYR* 1.3 79.6 - - - +
322D VAL* 1.3 64.3 + - - +
323D HIS 3.4 0.4 - - - -
324D GLU* 3.1 4.7 + - - +
325D ILE* 3.0 35.0 + - - +
391D ILE* 4.4 7.0 - - - -
392D ILE* 5.2 2.2 - - - -
397D ARG* 3.5 17.0 - - - +
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL* 3.5 49.1 - - + +
296D ILE* 3.7 26.8 - - + +
318D LEU* 2.8 28.6 + - + +
319D LYS 4.8 0.4 - - - +
320D TYR 3.5 0.6 - - - -
321D GLY* 1.3 75.8 - - - +
323D HIS* 1.3 78.4 + - + +
325D ILE* 3.3 5.5 + - - +
326D ILE* 3.0 34.1 + - + +
472D ILE* 4.0 13.5 - - + -
690E LEU* 6.0 0.2 - - + -
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Residues in contact with HIS 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D SER* 4.1 3.0 + - - -
319D LYS 4.8 2.2 + - - +
320D TYR 4.5 4.4 + - - +
321D GLY 3.4 0.6 - - - -
322D VAL* 1.3 86.1 - - + +
324D GLU* 1.3 62.9 + - - +
326D ILE* 3.7 14.4 - - + +
327D TYR* 3.0 45.9 + + + -
446D VAL* 4.0 21.5 - - + -
469D LEU* 4.1 5.7 - - + +
472D ILE* 3.5 35.0 - - + +
473D TYR* 3.1 34.4 + + - -
476D LEU* 4.9 4.6 - - - +
503D BRL 2.7 33.0 + - + -
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Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D TYR 3.8 3.1 + - - +
321D GLY 3.1 9.2 + - - +
323D HIS* 1.3 78.4 - - - +
325D ILE* 1.3 53.0 + - - +
327D TYR* 4.8 0.2 - - - -
328D THR* 2.7 34.8 + - - -
391D ILE* 3.3 16.8 - - + +
397D ARG* 2.8 38.1 + - - -
439D MET* 4.9 7.8 - - - +
442D LEU* 3.5 31.2 - - + +
443D ARG* 2.9 16.4 + - - -
446D VAL* 4.0 13.7 - - + -
477D TYR* 2.6 28.3 + - - +
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Residues in contact with ILE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PHE* 5.3 0.2 - - + -
296D ILE* 3.6 36.6 - - + -
321D GLY 3.0 18.7 + - - +
322D VAL 3.6 4.0 - - - +
324D GLU* 1.3 75.0 - - - +
326D ILE* 1.3 57.3 + - - +
328D THR* 2.9 7.6 + - - -
329D MET* 2.7 54.2 + - - +
388D ILE* 3.8 25.1 - - + +
391D ILE* 4.2 17.0 - - + -
392D ILE* 3.3 33.9 - - + -
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D SER* 3.4 34.1 - - - +
292D ALA* 3.8 14.8 - - + -
293D VAL* 4.3 2.0 - - + -
296D ILE* 3.8 13.9 - - + -
322D VAL* 3.0 31.1 + - + +
323D HIS* 3.7 18.6 - - + +
325D ILE* 1.3 76.1 - - - +
327D TYR* 1.3 70.5 + - + +
329D MET* 3.8 4.2 - - - +
330D LEU* 2.8 33.3 + - + +
503D BRL 4.0 29.2 - - + -
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Residues in contact with TYR 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323D HIS* 3.0 33.6 + + + +
324D GLU* 4.8 0.2 - - - -
326D ILE* 1.3 77.9 - - + +
328D THR* 1.3 66.4 + - - +
330D LEU* 3.6 13.0 + - + +
331D ALA 3.6 12.5 + - - -
367D LYS* 3.7 34.7 - - + +
370D PHE* 3.7 18.2 - - + -
442D LEU* 4.1 14.4 - - + -
445D ILE* 3.8 28.5 - - + -
446D VAL* 4.0 20.0 - - + -
449D HIS* 3.3 35.7 + - + -
473D TYR* 4.5 1.7 + - - -
503D BRL 3.8 31.9 - + + +
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Residues in contact with THR 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D GLU 2.7 20.1 + - - -
325D ILE* 2.9 11.3 + - - -
327D TYR* 1.3 77.6 - - - +
329D MET* 1.3 66.9 + - + +
331D ALA* 3.2 20.1 + - - +
332D SER* 4.0 2.9 + - - -
370D PHE* 4.2 8.5 - - - -
374D PHE* 3.5 33.9 - - + -
384D LEU* 4.4 8.9 - - + +
387D PHE* 3.9 16.6 - - + -
388D ILE* 5.1 4.9 - - + -
391D ILE* 3.9 4.7 - - - +
442D LEU* 3.1 21.3 - - - +
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Residues in contact with MET 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D TYR* 3.9 20.4 - - + +
226D PHE* 3.5 52.3 - - + -
228D LEU 5.6 4.7 - - - +
229D THR* 6.3 0.7 - - - -
296D ILE* 5.1 1.6 - - - -
325D ILE* 2.7 31.6 + - - +
326D ILE* 4.2 4.5 - - - +
328D THR* 1.3 69.6 - - + +
330D LEU* 1.3 65.7 + - - +
331D ALA 3.0 2.5 - - - -
332D SER* 3.0 27.1 + - - +
333D LEU* 3.7 9.6 + - - +
384D LEU* 6.0 4.3 - - + -
388D ILE* 3.4 28.0 - - + -
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D ILE* 2.8 19.4 + - + +
327D TYR* 3.6 17.9 - - + +
328D THR 3.2 0.2 - - - -
329D MET* 1.3 77.0 - - - +
331D ALA* 1.3 63.2 + - - +
333D LEU* 3.0 25.7 + - + +
334D MET* 3.4 36.1 + - + +
339D VAL* 4.1 14.8 - - + -
364D MET* 4.2 7.2 - - + -
367D LYS* 3.9 24.0 - - + -
503D BRL 3.5 39.7 - - + +
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 5.8 0.2 + - - -
327D TYR 3.6 6.7 + - - +
328D THR 3.2 14.5 + - - +
329D MET 3.0 0.2 - - - -
330D LEU* 1.3 79.6 - - - +
332D SER* 1.3 60.7 + - - +
334D MET* 3.0 13.0 + - - +
370D PHE* 4.6 1.6 - - + -
371D ALA* 3.6 36.1 - - + -
374D PHE* 4.0 14.4 - - + -
375D ASN* 3.2 31.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il